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    Vps54 VPS54 GARP complex subunit [ Mus musculus (house mouse) ]

    Gene ID: 245944, updated on 28-Oct-2024

    Summary

    Official Symbol
    Vps54provided by MGI
    Official Full Name
    VPS54 GARP complex subunitprovided by MGI
    Primary source
    MGI:MGI:2178798
    See related
    Ensembl:ENSMUSG00000020128 AllianceGenome:MGI:2178798
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    wr; Hcc8; mSLP8; Vps54l
    Summary
    Predicted to enable syntaxin binding activity. Involved in several processes, including chemical synaptic transmission; neurogenesis; and protein targeting. Acts upstream of or within musculoskeletal movement; neurofilament cytoskeleton organization; and regulation of growth. Part of GARP complex. Is active in mitochondrion. Used to study Werdnig-Hoffmann disease and amyotrophic lateral sclerosis type 1. Orthologous to human VPS54 (VPS54 subunit of GARP complex). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 6.9), bladder adult (RPKM 5.9) and 28 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Vps54 in Genome Data Viewer
    Location:
    11 A3.1; 11 13.89 cM
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (21189032..21271133)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (21239032..21321133)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_28838 Neighboring gene predicted gene 12040 Neighboring gene ribosomal protein, large, P0 pseudogene Neighboring gene STARR-seq mESC enhancer starr_28840 Neighboring gene predicted gene, 23582 Neighboring gene tudor and KH domain containing protein pseudogene Neighboring gene STARR-seq mESC enhancer starr_28841 Neighboring gene UDP-glucose pyrophosphorylase 2 Neighboring gene microRNA 1933 Neighboring gene STARR-positive B cell enhancer ABC_E5209 Neighboring gene STARR-seq mESC enhancer starr_28843 Neighboring gene STARR-seq mESC enhancer starr_28844 Neighboring gene heterogeneous nuclear ribonucleoprotein R pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    wobbler
    GeneReviews: Not available

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Gene trapped (1)  1 citation
    • Spontaneous (1) 

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • 5330404P15Rik

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables syntaxin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in Golgi to vacuole transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in L-glutamate import IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in apoptotic DNA fragmentation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in astrocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cellular response to progesterone stimulus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in homeostasis of number of cells IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within homeostasis of number of cells within a tissue IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in homeostasis of number of cells within a tissue IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in in utero embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular calcium ion homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in limb development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in limb morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within lysosomal transport ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    involved_in microglia differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mitochondrion organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in motor behavior IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in motor neuron apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within musculoskeletal movement IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of motor neuron apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neural tissue regeneration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neurofilament cytoskeleton organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neuroinflammatory response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neuromuscular synaptic transmission IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neuron apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neuron projection morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in post-embryonic forelimb morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein localization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein localization to cell surface IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein targeting to ER IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein targeting to lysosome IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein targeting to vacuole IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in respiratory electron transport chain IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to antibiotic IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to calcium ion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in retrograde transport, endosome to Golgi IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within retrograde transport, endosome to Golgi ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    involved_in skeletal muscle tissue development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in skeletal muscle tissue growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in spermatid differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sphingolipid catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in striated muscle contraction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in synaptic transmission, GABAergic IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in synaptic transmission, glutamatergic IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in thrombin-activated receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in ubiquitin recycling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in vacuole organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in vesicle-mediated cholesterol transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of GARP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of GARP complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of GARP complex ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    part_of GARP complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in mitochondrion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in trans-Golgi network ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    located_in trans-Golgi network ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    vacuolar protein sorting-associated protein 54
    Names
    tumor antigen SLP-8p homolog
    vacuolar protein sorting 54

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001290628.1NP_001277557.1  vacuolar protein sorting-associated protein 54 isoform 2

      See identical proteins and their annotated locations for NP_001277557.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AF424699, AK036667, AL669979, CJ134863
      Consensus CDS
      CCDS70147.1
      UniProtKB/TrEMBL
      Q91ZJ4
      Related
      ENSMUSP00000105206.2, ENSMUST00000109578.8
      Conserved Domains (1) summary
      pfam07928
      Location:727855
      Vps54; Vps54-like protein
    2. NM_139061.5NP_620692.3  vacuolar protein sorting-associated protein 54 isoform 1

      See identical proteins and their annotated locations for NP_620692.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AF424699, AK036667, AL669979, CJ134863
      Consensus CDS
      CCDS24463.1
      UniProtKB/Swiss-Prot
      Q5SPW0, Q8BPB3, Q8CFZ7, Q8CHL5, Q8R3R4, Q8R3X1
      UniProtKB/TrEMBL
      Q91ZJ4
      Related
      ENSMUSP00000006221.8, ENSMUST00000006221.14
      Conserved Domains (1) summary
      pfam07928
      Location:739867
      Vps54; Vps54-like protein

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      21189032..21271133
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011243720.2XP_011242022.1  vacuolar protein sorting-associated protein 54 isoform X1

      See identical proteins and their annotated locations for XP_011242022.1

      UniProtKB/Swiss-Prot
      Q5SPW0, Q8BPB3, Q8CFZ7, Q8CHL5, Q8R3R4, Q8R3X1
      UniProtKB/TrEMBL
      Q91ZJ4
      Conserved Domains (1) summary
      pfam07928
      Location:739867
      Vps54; Vps54-like protein
    2. XM_030246004.2XP_030101864.1  vacuolar protein sorting-associated protein 54 isoform X2

      UniProtKB/TrEMBL
      Q91ZJ4
      Conserved Domains (1) summary
      pfam07928
      Location:727855
      Vps54; Vps54-like protein
    3. XM_006514699.5XP_006514762.1  vacuolar protein sorting-associated protein 54 isoform X3

      UniProtKB/TrEMBL
      Q5SRW8
      Related
      ENSMUSP00000116739.2, ENSMUST00000132017.2
      Conserved Domains (1) summary
      pfam07928
      Location:573701
      Vps54; Vps54-like protein

    RNA

    1. XR_380966.5 RNA Sequence